Finally I will write my own little theory here. Always enjoyed reading and overall I think this site is an awesome idea. Curious to read all of the other theories. :-)

(Sorry for any mistakes as english is not my native language :-))

So first of all, Brett Partridge and Robert Kirkland are off the list.

I don't really buy into the ideas that Partridge faked his own death or that Michael Kirkland is Red John. Seems too simple for me, and Michael Kirkland is not on the list, which I think is true, as there are just not enough episodes left to have another twist and another twist and another twist in the story.

After "Red Listed" we now know that "Tyger Tyger" is the codeword for an underground government organization, with Reede Smith being a member of it. In "Black-Winged Redbird" we also saw McAllister, Smith and Bertram discussing stuff; which leads to the conclusion that these three are all part of the Tyger Tyger Collective.
They seem to have some connection to Red John. My theory is that the revelation of Red John would bring them into trouble somehow... to quote them in a scene: "How much does Jane really know?".

Smith also killed Kirkland, probably because they don't want Jane to get information from him. I don't know if they know the identity of Red John, but I think they have an interest in Jane NOT discovering who RJ is.

This leaves two names: Ray Haffner and Bret Stiles. 

A lot of things point to Haffner. He likes Lisbon (that would explain why he spared her and just drew the smile to scare Jane), he's a good whistler (as he leaves Lisbons room), he's involved with Visualize (Stiles had information about RJ).In the press release for the "Red John" episode and the episode before, there's an actor listed as "young man". You could say that from his looks that he may play a young Haffner at the Visualize farm back in the day.Haffner also had more appearance in the show than Bret Stiles. I think it would be smart to not pick a character who hasn't appeared in ages to be RJ.

Obviously there are more facts pointing to Haffner at the moment, but there are also some pointing to Stiles.

Stiles has the connections, charisma, mental abilities and intelligence to be someone like Red John. I don't really see these qualities in Ray Haffner. Out of all the suspects on the list, Stiles is the only one I could picture being able to be able to tool Jane like RJ does.

There's also a statement of Bruno Heller saying "we would be disappointed" if we find out who RJ is. This obviously can be interpreted in a lot of ways, but one could surely be: Bret Stiles is the only one capable of doing the complicated, intelligent things RJ does to fool Patrick all the time.

To conclude: I'm really split between Haffner and Stiles. It could be both of them. If I go with the facts I must say Haffner, but somehow my feeling tells me it's Stiles.

Thanks for reading :-)

At this point in time, Sheriff McAllister looks to me to be the most plausible Red John suspect.

I see that Brett Patridge may still be considered a suspect even though he's apparently dead. Even if he weren't dead, who was the guy who ambushed Lisbon while Patridge was obviously in his death throes? So it couldn't be Patridge.

It obviously wasn't Bob Kirkland given the events of Red Listed although the jury is still out on his twin brother. Assuming that the real RJ is restricted to Jane's list, I shall cross out Kirkland's brother as a suspect for now.

I think Gale Bertram is a little old to be running around committing murder. He's also a little too tall. That and Patrick Jane seems to be able to run intellectual circles around Bertram. The real RJ seems to be at least Patrick Jane's intellectual equal. Bertram doesn't seem to possess the necessary intellect that RJ clearly has.

Brett Stiles, while very intelligent, is also a little too old to be RJ. I don't see Stiles doing much by way of
hands on manual labour either (RJ has rough hands).

Ray Haffner may seem to be the best living suspect to fit RJs physical description but Patrick Jane made him look foolish when he was heading Jane's team. The real RJ wouldn't be so sloppy and foolish. Also, RJ is a very narcissistic character. I don't think he would have allowed Jane to intellectually dance around him as Jane did to Haffner without retribution of some sort.

Reede Smith doesn't fit the RJ description (although he is clearly mixed up in something sinister nonetheless). Smith is a little too pudgy and (while cunning) doesn't appear to be that smart.

Sheriff McAllister on the other hand steems to have quite the intellect. Look how he cleverly debated Jane as to the details of the body found in Season 6 Episode 3. Xander Berkley's portrayal of the McAllister character initially lead me to believe that he wasn't that smart. That changed in Episode 3. Physically, he could pull off RJs appearance although Haffner would be a better description. He is very adept at hunting.
And of course, he's afraid of pigeons.

If Bruno Heller is in fact telling us the truth that RJ is exclusively one of these suspects then I would have to bet on the Sheriff.

All those clues about Ray Haffner are good, I can agree with most of them that is why I won't repeat them, but the most striking one for me is :
RJ did not kill Lisbon, he doesn't do that and we know well that Haffner has feelings for Lisbon, that is why he left her alive.

For everyone out there that thinks Red John is  'many,' it does not matter. Jane wants the person who killed his wife and daughter, which is only one person. He will probably bring the Red John' associates to justice. If Red John consists of multiple people, then I would want to know the one person who killed his family more than the multiple people that make up Red John.

I made some observations, some of which are old and some of which are new. They make me feel that Red John is Haffner.

1. If you see the scene where Rosalind calls Jane and says "Roy is here", RJ sits with tea cup in his left hand. Look at the way he sits. Now compare this with the way Haffner sits when he visits Lisbon in her office. He sits exactly the same way. The camera will show you that for just a few seconds, when he is talking we see only his upper body. I think this could be a vital clue

2. He is a surveillance expert. He can watch people using all his resources, that is why he is ahead of Jane.

3. He was 21 and was in Elliston Farm when he was a member of visualize. He tells Lisbon that he doesn't believe that Brett Stiles is God, but happens to believe in somethings he says. All other members of Visualize believe Brett Stiles to be God, only RJ can say like this.

4. The way he walks in the hospital in Season 6 Episode 2 is exactly the same way Red John walks in Season 2 Episode finale, where he kills RJ copycats.

5. Well built, not too soft or too strong, his hands look exactly like Roy, medium aged man, height is just below 6, short hair, good looking. All this fits him.